The last NL team to have 3 pitchers in the top 5 in WAR among all players was the 1925 Reds. (Sean Forman found and sent me the list of all teams that had 3 or more in the top 10 just among pitchers and I went through those teams to see how they did among all players). Going through Baseball Reference year by year, it seems like 3 pitchers from one team in the top 10 in WAR among all players is very rare.

The 1966 Indians and the 1942 Tigers each had 5 in the top 10 among pitchers but none among all players.

The table below shows where these three Phillies pitchers rank in the NL in key stats so far this year.

Lee's 32nd in HR per 9 IP is in the top half of the 65 pitchers with 80+ IP. He gives up .79 HR per 9 IP while the league average is .877. Also note that the Phillies park gives up about 4% more HRs than average over the years 2008-10 (from the Bill James Handbook).

I think what Baseball Reference does is only include WAR from pitching activities when ranking pitchers. But when ranking all players the pitchers are evaluated using their pitching, hitting, fielding and baserunning.